New Beginnings
by MacGateFan
Summary: This was written for an LJ Weir ficathon which was originally titled The End of All Things. The prompt was write an end of Atlantis fic where Atlantis is under siege and someone from the team is there to comfort Elizabeth.


Title: New Beginnings  
Rating: PG  
Author: MacGateFan  
Author's note: This was written for an LJ Weir ficathon which was originally titled The End of All Things. The prompt was write an end of Atlantis fic where Atlantis is under siege and someone from the team is there to comfort Elizabeth.  
Disclaimers: All characters are property of people who aren't me.

* * *

"Elizabeth, go!" John Sheppard exclaimed, pushing her through the event horizon. She fell on her knees onto the ramp in Stargate Command and watched in horror as the Stargate shut off. She jumped when she felt a hand on her shoulder.

"Are you all right?" Teyla asked.

Elizabeth took a deep breath before replying. "I don't know. What happened? Why didn't John come through?"

"Everything happened so quickly. Perhaps Dr. McKay could explain."

For the first time since her arrival back on Earth, Elizabeth saw General Landry eyeing her in concern, Rodney and Carson behind him. She thought back to the calm before the storm...

* * *

"Are you sure about this, Rodney?"

"I would not make something like this up!"

Elizabeth looked at John. She couldn't believe that Atlantis was really going to sink back into the ocean. "And you haven't figured out why it's happening or how to stop it?" she asked.

"Zelenka and I have been working non stop since we learned about this. There is no way to prevent the sinking."

They all knew that if there were a way, Rodney and Zelenka would make it happen. "Just how much time do we have, Rodney?" John wanted to know.

"Three days. Five at most." Elizabeth took a deep breath as Rodney continued, more subdued. "Unfortunately, we have to admit defeat on this one. The ZPM does not have enough power to hold the shield up. Atlantis will be lost forever."

Elizabeth closed her eyes. When she opened them, she looked over at John again. "I'd like you to take Teyla to the mainland with you. Explain the situation to the Athosians. Give them the option of relocating in this galaxy or in ours."

"Got it."

"Dr. McKay, you know what you need to do." He nodded and the men left Elizabeth alone to her thoughts.

She sank into her chair. True, they could set up a new base in the Pegasus Galaxy, but without Atlantis would they survive a culling by the Wraith?

And would they survive the only connection to Earth by the Daedalus?

No, it looked like they had to return to the Milky Way. The only thing she kept thinking was how the Wraith had won.

* * *

Elizabeth woke up with a start. She looked at the clock and saw that it was still early. She knew she wasn't going back to sleep anytime soon.

Elizabeth longed to be on the balcony near her office in Atlantis. She longed to hear the door swish open and see John Sheppard grinning at her. She took a deep breath and shuffled to the kitchen.

Memories of Teyla and Rodney's last encounter with John began to surface as she turned on her coffee maker.

* * *

John glanced over at Teyla. She was staring silently out the window of the Jumper. "You okay?" he asked.

"I do not know what to make of this. The city of the Ancestors is actually sinking. It is unthinkable." She shook her head. "Never in my dreams have I imagined living in a different galaxy. I have a feeling many will want to return to Athos."

John was a bit surprised. "I thought the Wraith destroyed the land on Athos."

"They are a hearty people, Colonel. They will get through this just as they've gotten through everything else."

* * *

"Are you insane?"

"Rodney, someone has to do it!"

"Why does it have to be you? Why not someone who isn't important?"

John rolled his eyes. Rodney knew this had to be done. "This isn't Star Trek, no one person has a red shirt."

The scientist swallowed around the lump in his throat. He knew that. People didn't come back alive around here. "Let me do it, then."

"Now who's insane? Rodney, Earth needs you more than it needs me. The decision has been made. I'm staying here to make sure the self-destruct goes off and there's nothing left for the Wraith to find."

Rodney nodded, conceding defeat. "And don't tell Elizabeth!" John added.

He nodded again. "She's going to kick my ass."

"I can kick it right now."

"Fine!" he growled. Rodney calmed himself and looked at his friend. "I don't mean to sound mushy or anything, but you've been a great friend."

"I hear ya," John replied.

Rodney was going to shake John's hand, but his friend pulled him into a bear hug instead. The only thing Rodney kept thinking was that Elizabeth Weir was going to kill him when she learned of the plan.

* * *

Elizabeth watched as the last of the equipment and personnel left Atlantis. She never thought this day would come. At least not so soon. "How are you holding up, Love?"

"I've been better," she replied, turning to face Carson. "My staff is gone, but I wanted to see you before I left. Elizabeth it's been a pleasure working with you."

She smiled and gave him a hug. "You too, Carson. I just wish it didn't have to end this way."

"Aye," he replied sadly. "I'll see you back on Earth."

She watched as he ran down the stairs and waved as he ducked into the 'Gate. As soon as he disappeared, a tremor shook the city.

John and Rodney ran up to her. "We need to go!" Rodney exclaimed. The city shook more and Rodney fled down the stairs to the 'Gate. "Come on!"

John shook his head. "Never fails."

Elizabeth grinned as they both followed Rodney's path. She turned to see John standing in the middle of the room. "John, what are you doing?"

"Don't worry about me, just go!"

"John!"

He ignored her plea and grabbed her hand, pulling her towards the event horizon. "Elizabeth, go!"

The coffee cup she was holding suddenly crashed to the floor. She ignored it and sank to her knees, crying uncontrollably. She couldn't believe Atlantis and John Sheppard were both gone. How could she just go about her daily life when she couldn't have either?

She barely felt the strong arms that lifted her to her feet and were holding her close. The smell was immediately recognizable. Opening her eyes, she nearly had a heart attack. "John."

He smiled and helped her to the couch. "Hey. Did you miss me?" Instead of replying, she smacked him across the face. "Ouch! What was that for?"

"Scaring the crap out of me John Sheppard! I wish you would have told me what you were planning!"

"I didn't think you would have let me do it. Hell, I didn't even think I'd make it back! I wanted to make certain the Wraith never found Atlantis or be able to use the 'Gate to come here. I'm just glad everyone made it back safely. Especially you."

Elizabeth nodded. "You'll have to tell me how you did get back here one day." She paused a moment. "Wait, you said 'especially you'. What's so special about me?"

"I think you know, Elizabeth." She blushed under his scrutiny. "You already miss it, don't you?"

"I missed it the minute I stepped into the Gateroom at the SGC, but I think I have the best part with me now."

John crossed his arms and pouted. "Rodney doesn't count."

She laughed. "No, he's definitely not the best part!"

John laughed with her and two snuggled close together. "Does he know you're back?"

"Not yet, but I'm sure he will when we meet for debriefing tomorrow."

Elizabeth sighed as John played with her hair. "He's going to be so angry at you."

"I know." They sat in content silence for a bit until Elizabeth said his name. "Yeah?"

"I love you."

He leaned in to kiss her. "I love you too."

* * *

The Debriefing

Rodney looked around the room at the former Atlantis expedition team members. Only one was missing and it made him feel beyond miserable. He had no idea when he started thinking of John Sheppard as his friend, but he knew no one would be able to replace him.

General Landry entered the room, tearing Rodney from his thoughts. "We're waiting on one more person, he just checked in upstairs, and then we'll get started."

Rodney shared a glance with Carson and Teyla, wondering whom it could be. From the look on Elizabeth's face, she seemed to already know. He also noticed a slight tinge of pink to her cheeks. He would definitely have to ask her about that later.

"Sorry, I'm late, but I'm not used to driving in traffic."

"Bloody hell!" Carson exclaimed in shock.

Landry and Elizabeth watched their faces in amusement. Suddenly, Rodney's face was bright red and he walked over to his friend. For a brief moment, Elizabeth thought he was actually going to hit John in the face.

"Oh thank God!" Rodney cried, hugging him. He then punched the pilot in the arm. "Don't scare us like that again!"

"I agree, Colonel," Carson said, "You should know that I nearly had a heart attack two days in a row because of you!"

John looked apologetic. "I'm sorry. I really didn't think I was going to get out of there alive."

Landry interrupted. "Colonel, why don't you have a seat and start from where everyone had left the city."

John nodded, taking a seat. "Yes, Sir."

"After sending everyone through the 'Gate, I rushed up the stairs to make sure everything was going smoothly. As I was waiting for the inevitable, a flash of light surrounded me and I was on the Daedalus."

"Wait, I thought the Daedalus was out of commission for awhile," Rodney said.

"That's what I thought too," John replied. "Apparently repairs were still under way as it headed to Atlantis. The communications array was down so they couldn't contact me to let us know what was going on. Frankly, they didn't think they'd get there in time to save anyone."

Landry smiled. "Let's just be glad they did, Colonel." He then looked at each of the people around the table. "I truly am sorry that this had to end the way it did. We do intend on sending a team out in a few weeks to check the damages and make certain the Wraith won't be able to access the 'Gate.

"Until then," Landry stood up, "there will be a banquet celebration in honor of the men and women who lost their lives. Any questions?"

"Assignments, Sir?"

"I'm assuming you'd like to form an SG team, Colonel. Your choice of members."

John was a bit surprised that he would be able to choose his own team, but nodded enthusiastically. "I just want to warn you, Sir, that my team tends to get into a lot of trouble."

"Then you'll fit in just fine here," Landry, replied with a laugh.

* * *

Teyla walked down the halls of the SGC. She missed her people terribly, but for now she would remain on Earth until they could travel to the Pegasus Galaxy. She was able to find her way to the gym with little difficulty and was surprised to see another whom she sensed was not human.

He turned to face her. "You are Teyla Emmagan."

"I am."

He bowed his head. "I am Teal'c."

"You are not of this planet?" she asked.

"Indeed I am not. I am from a planet called Chulak. I have not been there for quite some time."

Teyla smiled sadly. "I am from Athos and I have not been there for many days. Do you like it here? On Earth?"

Teal'c seemed to be thinking for a moment before he spoke up. "It does take time to get used to, but I do enjoy this planet. The people are a very determined race."

"I could not agree more, Teal'c."

John arrived in the gym to see that a crowd had formed. He spotted Colonel Mitchell and moved through everyone towards his friend. "Hey Cam, what's going on?"

Mitchell pointed. "Teal'c and Teyla have been at it for about a half hour. Neither seem to be breaking a sweat."

John watched as Teyla pivoted to the right while Teal'c moved to the left. That's when he saw it coming, most likely because he had been on the receiving end of this particular brand of attack from the Athosian.

"I bet you a week's pay that Teyla is going to sweep Teal'c off his feet," John said. Mitchell merely stared at his friend in disbelief. "What? If you really trust in Teal'c's abilities, then take the bet."

"You're on!" Mitchell replied, shaking John's hand. Just as he did, Teal'c dropped to the floor.

John grinned and shoved his hands in his pocket, whistling on his way out the door.

* * *

John looked back at his team as the arrived on the first planet since being back on Earth. Rodney was whining about the heat, Teyla was scanning the treeline, and Elizabeth eyes were shining with wonder.

He was kind of surprised when she expressed interest in joining the team. He had asked her if she thought Carson should join them, but then she asked him if she could instead. John was hesitant at first, but finally agreed when she mentioned they could use a negotiator.

Yeah. Because sometimes negotiating for John Sheppard included firing a P-90.

"I knew I should have declined coming to this planet," Rodney complained. "It's too swampy and I just know I'm going to catch malaria!"

"Relax, Rodney. Besides, did you not say there were some energy readings worth studying?"

John and Elizabeth smiled gratefully at Teyla. "Why don't you two check out the energy readings while Elizabeth and I see if we can find any signs of intelligent life?"

"Very well, Colonel," Teyla replied.

Once they were alone, John took Elizabeth's hand and they headed in the opposite direction. "I thought we were going to look for signs of intelligent life."

"Oh, we are, but I can't help what may happen during that search."

Elizabeth sighed happily as John's lips met hers. She never thought anything could feel so right. Elizabeth felt John tense and immediately knew something was wrong. "John?" Instead of replying, he was falling to his knees. "John!" she cried again.

She quickly scanned the area and finding no one, she called Teyla and Rodney, frantically trying to snap John out of his pain induced haze. "Elizabeth, are you all right?" Rodney's voice called over the radio.

"John's been injured but I don't know what happened. We may not be alone!" She cried as her heart thumped wildly in her chest.

"We are on our way," Teyla responded.

Elizabeth suddenly realized where John was injured when she felt something wet and sticky on his back. Blood. "Oh God! John! John, answer me, please!"

She received a groan in response just as Rodney and Teyla arrived. Teyla began circling the area, but did not see anyone around. "Hurry," she said, "we must get him to the 'Gate before they begin firing again."

"John, we're going back to Earth," Elizabeth said. She saw that he was barely conscious, but was able to nod slowly.

Rodney helped Elizabeth lift him from the ground. He glanced at John's face to see a sheen of sweat on the man's forehead. He looked back at Teyla. "We're ready."

"Let us go then!" she exclaimed.

* * *

General Landry joined them in the infirmary. "Doctors, Teyla," he said with a nod. "Any word on Colonel Sheppard's condition?"

"Not yet, General," Elizabeth replied. He saw that her eyes were red from crying. "They almost lost him twice."

"What happened?" he asked.

Elizabeth shook her head. "I don't know. One minute we were… talking, the next he was falling to his knees. Whatever weapon they used, it was silent."

No one said anything after that, each one lost in thought. Carson came out a few minutes later looking a little weary. Elizabeth immediately walked over to him. "How is he, Carson?"

"He's in critical condition, I'm afraid. The bullet was lodged near his heart. He was having trouble breathing so he's on a respirator for the moment. We're monitoring his heart rate and he's been given antibiotics to stave off any infection."

"May we see him?" Teyla asked.

"Aye, but not for long."

This wasn't the first time General Landry witnessed such closeness between team members. In fact, he saw it with SG-1, but this seemed different somehow. He felt like an intruder.

The Atlantis Expedition team had a bond that could never be broken. After spending the first year alone, cut off from Earth, they had learned to rely on one another in more ways than one could imagine.

Landry decided to give them some time on their own. He could read the report later. The man was so lost in thought that he nearly slammed into Samantha Carter. "Sorry, Colonel, I wasn't paying attention."

"Me neither, Sir," she said.

He noted that she was holding her arm. "What happened?"

"P3X452 has same rather nasty thorn bushes near the Stargate. I, unfortunately had a run in with them."

"Then I'll let you get to the infirmary."

She nodded. "Thank you, Sir."

Rodney muttered something about changing and getting to work on some experiment and rushed out the door. His eyes widened when he saw Samantha Carter looking quite lovely. He had actually not seen her since they arrived back on Earth.

"Welcome home, McKay," she said.

He snorted. "Yeah, thanks."

"Are you all right?"

Rodney glared at her. Right now he just wasn't in the mood to deal with anyone and Sam had come at the worst time. "No I'm not, if you must know! My best friend is dying and our home was destroyed!"

Before Sam could reply, he was gone. She stared after him in shocked silence and didn't notice Teyla next to her. "From what Dr. Weir and Colonel Sheppard have told me, Rodney has changed a great deal since you've known him. Please do not take his outburst personally."

"I won't," she replied, walking over to the nurse.

"Teyla, Love, is everything all right?"

"Rodney is having a difficult time with this."

"Aye," Carson said. "Perhaps you could keep an eye on him? Make certain he gets some rest."

Teyla nodded. "I can do that."

* * *

Elizabeth had firmly planted herself in the seat next to John's bed, holding onto his hand for dear life. This was her fault. She shouldn't have insisted on going off world. Now he was lying in the infirmary fighting for his life.

"I'm so sorry, John," she whispered, tears falling down her cheeks. "Please don't leave me. I love you."

Her only response was the steady beep of the heart monitor. Elizabeth moved the chair closer to the bed, resting her head near his hand, falling asleep.

That's where Carson found her when he came in to check on his patient. He was careful not to wake her up, but soon Elizabeth was stirring. "Carson?"

"Aye, Love."

"How's he doing?"

"Much better. His heart rate has improved vastly." He eyed her in concern. "Are you all right?"

She nodded, eyes cast to the bandage on his back that Carson was changing. "It's my fault."

"Excuse me?" Carson wasn't sure he heard her correctly.

"It's my fault," she said louder.

"Now hold on a minute, Elizabeth," Carson said, moving to her side. "Don't blame yourself for something you couldn't control!"

"But that's just it, I could have controlled it! Carson, we were kissing when John was shot!"

He stared at her. No wonder why she was thinking like that. "It's still not your fault, Elizabeth. Whoever shot at you were very good at what they did, they had silent weapons. Now I know Colonel Sheppard can usually detect the bad guys, but even he isn't perfect."

"I know that… It's just… Either way we should have been paying more attention to our surroundings. What if Rodney and Teyla had needed our help, but we were too wrapped up in ourselves to get to them right away?"

Elizabeth took a breath. "I am going to take myself off the team, Carson. There's nothing you can say to make me change my mind."

"You do what you feel is best," he replied with a sigh.

The first thing he noticed while he was waking was the pressure on his right hand. Opening his eyes, John smiled. Elizabeth was sleeping soundly. He brushed a strand of hair from her eyes, causing her to stir.

"Hmm… John?" she said, blinking. A grinned formed on her face as her eyes widened. Before he could say anything to her, Elizabeth took his face in her hands and kissed his lips deeply.

"Wow!" John said after a few minutes. "I should be unconscious more often."

Elizabeth smacked his arm. "Don't joke like that! We almost lost you! Again!"

"Sorry," he replied sheepishly. "How long was I out of it this time?"

"Two days, Colonel." John looked up to see Carson head over and begin checking his patient's vitals. "You have the worst luck, yet the best, Son."

Elizabeth watched the exchange. She had never been more relieved her entire life. She couldn't wait to tell him about the commendation he was going to receive at the banquet.

"Everything seems to check out, Colonel. You're free to go the banquet tomorrow, but I don't want you overdoing it and I don't want you drinking any alcohol."

"Doc," John said, "you know me…"

Carson held up his hand. "Stop right there. Aye, I know you and I'm telling you again, no alcohol."

"I'll keep an eye on him, Carson," Elizabeth told the physician.

* * *

"I didn't even know they had a banquet hall down here," Rodney said, happily eating a piece of chocolate cake.

John shook his head. "You keep eating like that and we'll have to roll you out of here, Rodney."

"Stop being mean! Do you know how long I have waited to eat a pure honest to goodness chocolate cake?"

Teyla and Elizabeth smiled at one another, enjoying the banter between the two friends. Despite Atlantis being gone, they were still able to joke and have fun. The fact that they were all alive made this night even more special.

"Ladies and gentlemen, may I have your attention please." Everyone stopped talking as General Landry began. "Tonight we commemorate the men and women of the Atlantis Expedition team. From those with us here tonight to those who died in the service of our planet."

Landry then began reading off every name beginning with Aiden Ford. John looked dejectedly at his untouched dessert. Ford would never be able to enjoy this cake or another one like it. What had happened to his friend?

John looked to his right when he felt a hand on his shoulder. Elizabeth smiled at him and nodded her head towards General Landry. She wanted him to pay attention because she had decided to keep this information a surprise.

"There is one last commendation that the President would like to award himself. Mr. President."

"Dr. Weir, Atlantis expedition members, I would like to take this opportunity to thank you for the fine work you all accomplished while serving in the Pegasus Galaxy. I am deeply saddened that it had to end the way it did.

"Today is with great pleasure that I award one of your team members with the Medal of Honor. The Medal of Honor is awarded to a person who distinguishes himself conspicuously by gallantry and intrepidity at the risk of his life above and beyond the call of duty while engaged in action against an enemy of the United States or while engaged in military operations involving conflict with an opposing foreign force. The deed performed must be one of personal bravery or self-sacrifice.

"Many of us never thought this man would even go pass the rank of "Captain", but here we are years later and he's a lieutenant colonel. This Medal of Honor is awarded to Lieutenant Colonel John Sheppard."

John sat in shocked silence for a few minutes. Finally Elizabeth whispered in his ear. "That's you, John."

"Right."

Rodney stood to help him up. "Come on," he said, "lets get you your pretty medal."

John still couldn't believe this was happening as he stepped onto the makeshift stage. Here he was accepting the Medal of Honor from the President of the United States. "Congratulations, Colonel," President Hayes said. "I've read every one of your mission reports and you've earned this many times over. Excellent work."

"Thank you, Sir," John replied.

* * *

The woman sat in silence as she watched her son receive the Medal of Honor. She still couldn't believe he was standing there alive. After John was listed as MIA in Afghanistan, her husband told her no one would be going after him and that he was lost to them forever.

But when General O'Neill arrived at her home with tales of a top-secret mission that involved her only son, Christina Sheppard could hardly believe it. If her husband were still alive she would have smacked him so hard, his head would be spinning.

She later found out from her daughter, Bridgette, that John had attempted to see them when he had returned, but David would not let him in and threatened the poor teenager into silence. Bridgette felt horrible about it. In fact, she had attempted to write to her brother, but the letters came back unopened.

"Mom, are you ready?"

Christina nodded. "As ready as I'll ever be," she replied. "I only hope he is."

* * *

"John," Elizabeth called.

When the congratulators had finally moved away, he turned to face her. "Remember that surprise General O'Neill had for you?"

"You mean there's something else beside this?" he asked, pointing at the medal on his chest.

She smiled, taking his hand. "Yes. There are two very important people who would like to meet with you."

"Who?"

"Be patient!"

"You know that's not one of my strong suits."

"I know, John," Elizabeth replied with a laugh. "Now quiet so I can tell you about them before you go in and pass out from complete shock."

John stared at her. Who could possibly be in a VIP suite that would cause him to pass out from shock? "So?"

"John, General O'Neill found your Mother and sister."

Okay, that would do it, he thought as his mind spun. The last time he saw them he was leaving for Afghanistan.

"John?"

He blinked. "I'm all right. But my Dad said… my Dad said they were dead."

"What?" Elizabeth asked. She didn't know about that. How could anyone lie to their child about something like that? Elizabeth took his hands in hers. "Take a deep breath. They're alive, John. Be grateful. We can deal with the mess your Father created later, all right?"

"Yeah," he replied, kissing her softly on the lips. "I love you."

"I love you too."

A moment later, John took another deep breath and with a nod from Elizabeth, opened the door. He felt the pull of his stitches, but right now he didn't care, as he held tight to his Mom. "Oh, John!" she whispered.

"Mom, I've missed you so much!"

Bridgette watched them with tears in her eyes. She could hardly believe that her big brother was standing there in front of them after all these years. She moved closer, tapping him on the shoulder.

"Hey, Bed Head," she said; calling him by the nickname she gave him so long ago.

"Bridgette!" John exclaimed, pulling her in the hug.

* * *

Elizabeth went to the VIP suite she left John. He'd been in there for two hours so hopefully they were finished debriefing each other. Taking a deep breath, she knocked on the door. Elizabeth heard John telling her to come in.

The smile on his face grew wider as Elizabeth stepped into the room. He immediately went over to her and took her hand. "Mom, Bridgette, this is Dr. Elizabeth Weir. Elizabeth, this is my Mom, Christina and my sister, Bridgette."

Christina smiled knowingly. She could tell from the expression her son's face that this was the woman he was going to spend the rest of his life with. "It's lovely to meet you, dear," Christina said.

"Likewise," Elizabeth responded. She glanced at John and grinned. "It's time."

"Time for what?" John asked, a little worried about that goofy grin Elizabeth had on her face.

"To exchange embarrassing stories about you, sweetheart," Christina replied.

John shook his head. "Oh no, I don't think so!"

Bridgette took his hand and led him to the couch. "Sit!" she ordered. "You will stay there until we're finished."

"What did I do to deserve this?" he muttered, sinking onto the couch.

"It's because we love you, John," Elizabeth replied.

* * *

Thanks for reading! I've ended it here for now, but I would love feedback on if I should continue this or not.  
Michelle 


End file.
